Hello All,

I am running the following code under R.2.11.1 on a Dell PowerEdge 2900 III
running Windows 2003 Server 64-bit OS (Release 2 build 3790) with 48GB RAM.

When I try an get HPD intervals for my model using mcmcsamp() I get the
following error: "Error in .local(object, n, verbose, ...) : Update not yet
written"

I have searched the R-help & R-sig-mixed archives; I have googled the
specific error (and found some threads in R-help dating to 2008-2009
suggesting the author of the code put this message in mcmcsamp to remind him
to finish coding a particular part of mcmcsamp); I have examined the lme4
documentation (and mcmcsamp); I have read the R FAQ; and I have consulted
with my boss PhD biostatistician (he suggested I make a post). As mentioned,
I did run across a number of conversations dating to 2008-2009 regarding
this error, but did not see a suggestion. I did see something to the effect
that it was to remind the programmer he needed to finish some coding. Was
the code ever finished/updated? Is the issue still outstanding? I have tried
installing lm4a from R-forge and ran into the following error:

> install.packages("lma4", repos="http://R-Forge.R-project.org")
Warning: unable to access index for repository
http://R-Forge.R-project.org/bin/windows64/contrib/2.11
Warning message:
In getDependencies(pkgs, dependencies, available, lib) :
  package ‘lma4’ is not available

when I researched this error it was suggested I install "Rccp" from R-forge.
I tried this and received the following error:

> install.packages("Rcpp", repos="http://R-Forge.R-project.org")
Warning: unable to access index for repository
http://R-Forge.R-project.org/bin/windows64/contrib/2.11
Warning message:
In getDependencies(pkgs, dependencies, available, lib) :
  package ‘Rcpp’ is not available

Where am I going wrong in the process? What have I missed? Is this a problem
with my data? I have run a similar regression with continuous A1c data
(range: 3 to 18) as the dependent variable and had no problems for all my
data (n=700K observations and 5 time points). I also ran the data for 1%,
5%, 10%, and 25% random samples or the data, with a continuous dependent
variable) and had no problems generating CIs. I am not wedded to mcmcsamp()
& HPDinterval(), but I understand it is one of the more robust methods of
generating CIs about beta for mixed effects models. I am happy to use any
approach as long as statistically valid.

Any status or updates would be greatly appreciated.

Thanks in advance.

Greg Gilbert


> options(repos="http://lib.stat.cmu.edu/R/CRAN/")
> myPackages <- c("lme4", "foreign", "Hmisc")
> install.packages(myPackages, dependencies=TRUE)
> update.packages(checkBuilt=TRUE, ask=FALSE)
> library(foreign)
> library(Hmisc)
> library(lme4)
>
> cohort <- sasxport.get("//v07.med.va.gov/cha/TREP/___neworganization/workgroups/wg10_06_sampling_gebregziabher/data/PCT01SRS.xpt")
Processing SAS dataset PCT01SRS          ..
> ## time is 1 to 5
> cohort$time.ctr.sq <-(cohort$time-3)*(cohort$time-3)
> attach(cohort)
> ## a1cge8 is 0, 1
> ## id is 4-7 digit number
> ## age is continuous 18-103
> ## svcpct is continuous 0 to 100
> ## all other variables are binary 0, 1
> f  <- a1cge8 ~  (1|id)   + time       + time.ctr.sq     +
+                 nhb      + hispanic   + other           +
+                 male     + age        + mstat           +
+                 svcpct   + urban      +
+                 abuse    + anemia     + cancer          +
+                 cbd      + chf        + cvd             +
+                 depress  + htn        + hypothy         +
+                 liver    + lung       + lytes           +
+                 obese    + other.dz   + psych           +
+                 pvd
>
> ## finite population correction
> population <- 890394
> sample     <-   9000
> fpp        <- sqrt((population-sample)/(population-1))
>
> fit        <- lmer(f, family=binomial(link="logit"), data=cohort)
>
>    mcmc.ci <- mcmcsamp(fit, 1000)
Error in .local(object, n, verbose, ...) : Update not yet written
> ci         <- HPDinterval(mcmc.ci)
Error: object 'mcmc.ci' not found
Error in HPDinterval(mcmc.ci) :
  error in evaluating the argument 'object' in selecting a method for
function 'HPDinterval'
>

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